You have to create your own implementation of an org.eclipse.emf.compare.diff.engine.GenericDiffEngine (simply extend the Generic one), and override its "getAttributeChecker' so that it returns your own implementation of the org.eclipse.emf.compare.diff.engine.check.AttributesCheck class, where you will override the "shouldBeIgnored(EAttribute)" method.

After that, override the "org.eclipse.emf.compare.diff.engine" extension point and provide your own engine to EMF Compare.